Transient-time analysis of substrate-channelling in interacting enzyme systems.

The kinetics of dynamically interacting enzyme systems is examined, in the light of increasing evidence attesting to the widespread occurrence of this mode of organization in vivo. The transient time, a key phenomenological parameter for the coupled reaction, is expressed as a function of the lifetime of the intermediate substrate. The relationships between the transient time and the pseudo-first-order rate constants for the coupled reaction by the complexed and uncomplexed enzyme species are indicative of the mechanism of intermediate transfer ('channelling'). In a dynamically interacting enzyme system these kinetic parameters are composite functions of those for the processes catalysed by the complex and by the separated enzymes. The mathematical paradigm can be extended to a linear sequence of N coupled reactions catalysed by dynamically (pair-wise) interacting enzymes.     

Kinetic analysis of enzyme reactions with slow-binding inhibition.

In this paper we present a general kinetic study of slow-binding inhibition processes, i.e. enzyme reactions that do not respond instantly to the presence of a competitive inhibitor. The analysis that we present is based on the equation that describes the formation of products with time in each case on the experimental progress curve. It is carried out under the condition of limiting enzyme concentration and allows the discrimination between the different cases of slow-binding inhibition. The mechanism in which the formation of complex enzyme-inhibitor is a single or two slow steps or follow a rapid equilibrium, has been considered. The corresponding explicit equations of each case have been obtained and checked by numerical integration. A kinetic data analysis to evaluate the corresponding kinetic parameters is suggested. We illustrate the method, numerically by computer simulation, of the reaction and present some numerical examples that demonstrate the applicability of our procedure.     

Characterization of "thyroliberin-deamidating enzyme" as a post-proline-cleaving enzyme. Partial purification and enzyme-chemical analysis of the enzyme from anterior pituitary tissue.

An enzyme which catalyzes the deamidation of thyroliberin (TRF; less than Glu-His-Pro-NH2) has been purified 110-fold from extracts of bovine anterior pituitary by ammonium sulfate fractionation, ion exchange chromatography on DEAE-cellulose, and gel filtration. This enzyme of 76,000 molecular weight (as estimated by gel filtration) exhibits maximal activity at neutral pH (optimum pH 7.4 to 7.6) in buffers of high ionic strength supplemented with thiol-protecting agents. As indicated by the strong inhibition of the enzymatic activity by N-ethylmaleimide and Hg2+, as well as by the extreme sensitivity toward diisopropyl fluorophosphate, -SH, and -OH residues apparently represent essential functional groups of the enzyme. The stereospecific deamidation of TRF (Km = 4.1 . 10(-4) M) is inhibited competitively by TRF analogues which contain proline or by the proline containing biologically active peptides luliberin (LH-RF), oxytocin, vasopressin, angiotensin II, and Substance P. TRF analogues without proline or peptide amides without proline are ineffective. This enzyme cleaves the appropriate Pro-X bonds in luliberin, angiotensin II, pyroGlu-His-Pro-Gly-NH2, and the collagenase substrate Z-Gly-Pro-Leu-Gly-Pro. Thus, it may be characterized as a post-proline-cleaving enzyme.     

Rapid enzyme hydrolysis of urine extracts for estriol analysis.

A method is described for quantitatively hydrolyzing estriol glucosiduronate (and presumably other urinary steroid glucosiduronates and sulfates) in 2 hr after concentration of the urine and removal of enzyme inhibitors by passage over a column of XAD-2 resin. The estriol is sufficiently pure for direct GLC or mass spectrometry analysis.     

Multilocus enzyme electrophoresis analysis ofPseudomonas syringae pv.phaseolicola

A multilocus enzyme electrophoresis technique was developed to detect variation in seven enzyme loci among isolates ofPseudomonas syringae pv.phaseolicola, representing three races from different geographical locations, the causal agent of the halo blight disease of beans. Cellulose acetate gel electrophoresis of seven enzymes revealed 19 electrotypes (ET) among 21Pseudomonas syringae pv.phaseolicola isolates. One of the pathovarsyringae and one of the pathovartomato isolates were represented by two different ET. The population of Turkish isolates and three races of the pathovarphaseolicola appeared to be genetically diverse.     

Metabolic control analysis. The effects of high enzyme concentrations

Differing views have been given in the literature as to whether the presence in a pathway of an enzyme at a concentration comparable to that of its substrate affects the values of control coefficients and the theorems of metabolic control analysis. Here we argue in favour of one of those views: that there is no effect unless the enzyme sequesters a substrate that contains a conserved moiety. In this particular case, we derive both a general criterion for estimating whether such an effect will be of a significant magnitude, and equations for determining the changes in the flux control coefficients. The nature of the phenomenom and the application of the equations are illustrated with a numerical simulation.     

Restriction enzyme analysis of mitochondrial DNA in colorectal tumours.

Total cellular DNA samples were isolated from 15 colorectal adenocarcinomas, 8 colon adenomas and their adjacent histologically normal colon mucosa. These DNA samples were digested separately with 13 different restriction endonucleases and analysed by Southern blot hybridization using a purified 32P-labelled human mtDNA probe. The fragment patterns from tumour mtDNA were compared to those from corresponding normal mtDNA. No evidence for large deletions, insertions, rearrangements or single base mutations in the detectable regions was detected. This suggests that other mechanisms may be responsible for the changes of colorectal tumour mitochondria.     

Theoretical and experimental analysis of a soluble enzyme membrane reactor.

Recently enzyme immobilization techniques have been proposed that are mainly founded on the formation of an enzyme-gel layer onto the active surface of an ultrafiltration membrane within an unstirred ultrafiltration cell. If the membrane molecular-weight cutoff is less than the enzyme molecular weight and hence such as to completely prevent enzyme permeation (once the enzyme solution has been charged into the test cell and pressure applied to the system), a time progressive increase in enzyme concentration takes place at the upstream membrane surface that can eventually lead to gelation and hence to enzyme immobilization. However, depending on the total enzyme amount fed, the maximum enzyme concentration achieved in the unsteady state could be less than the gelation level. In this situation, no immobilization occurs and the enzyme still remains in the soluble form although it is practically confined within a limited region immediately upstream the membrane and at fairly high concentrations. In this paper, the experimental conditions that allow gelling to occur are discussed together with a theoretical analysis of the soluble enzyme membrane reactor which is obtained when no gelling takes place. Such a system could be usefully employed in performing kinetic analyses at high enzyme concentration levels that are still in the soluble form.     

Restriction enzyme analysis of Bacillus subtilis ribosomal ribonucleic acid genes.

The organization of the ribosomal ribonucleic acid (rRNA) genes (rDNA) of Bacillus subtilis was examined by cleaving the genome with several restriction endonucleases. The rDNA sequences were assayed by hybridization with purified radioactive rRNA's. Our interpretation of the resulting electrophoretic patterns is strengthened by an analysis of a fragment of B. subtilis rDNA cloned in Escherichia coli. The results indicated that there are eight rRNA operons in B. subtilis. Each operon contains one copy of the sequences coding for 16S, 23S, and 5S rRNA. The sequences coding for 5S rRNA were shown to be more closely linked to the 23S rRNA genes than to the 16S rRNA genes.     

Immobilized enzyme cellulose hollow fibers: II. Kinetic analysis

Immobilized enzyme hollow fibers may be useful in the purification or treatment of whole blood under clinical conditions. In this study, catalytically pure heparinase was immobilized to cellulose to analyze the feasibility for the removal of heparin's anticoagulant activity from whole blood. The kinetics of catalytically pure heparinase immobilized to regenerated cellulose hollow fibers were quantified with respect to mass transfer coefficient and enzyme loading. The kinetic analysis showed that increases in the mass transfer coefficient of heparin in the fiber lumen decreased the apparent Michaelis constant while increases in enzyme activity immobilized to the fiber lumen increased the apparent Michaelis constant. The apparent Michaelis constant was an order of magnitude greater than the intrinsic K(m) value for the system. The intrinsic K(m) value for heparinase-cellulose is 0.4 +/- 0.3 mg/mL (N = 6) and it is the same order of magnitude as the K(m) value for soluble heparinase.     

Biochemical analysis of the modular enzyme inosine 5'-monophosphate dehydrogenase.

Two prominent domains have been identified in the X-ray crystal structure of inosine-5'-monophosphate dehydrogenase (IMPDH), a core domain consisting of an alpha/beta barrel which contains the active site and an inserted subdomain whose structure is less well defined. The core domain encompassing amino acids 1-108 and 244-514 of wild-type human IMPDH (II) connected by the tetrapeptide linker Ile-Arg-Thr-Gly was expressed. The subdomain including amino acids 99-244 of human wild-type IMPDH (II) was expressed as a His-tagged fusion protein, where the His-tag was removable by enterokinase cleavage. These two proteins as well as wild-type human IMPDH (II), all proteins expressed in Escherichia coli, have been purified to apparent homogeneity. Both the wild-type and core domain proteins are tetrameric and have very similar enzymatic activities. In contrast, the subdomain migrates as a monomer or dimer on a gel filtration column and lacks enzymatic activity. Circular dichroism spectropolarimetry indicates that the core domain retains secondary structure very similar to full-length IMPDH, with 30% alpha-helix and 30% beta-sheet vs 33% alpha-helix and 29% beta-sheet for wild-type protein. Again, the subdomain protein is distinguished from both wild-type and core domain proteins by its content of secondary structure, with only 15% each of alpha-helix and beta-sheet. These studies demonstrate that the core domain of IMPDH expressed separately is both structurally intact and enzymatically active. The availability of the modules of IMPDH will aid in dissecting the architecture of this enzyme of the de novo purine nucleotide biosynthetic pathway, which is an important target for immunosuppressive and antiviral drugs.     

Kinetic analysis of experiments involving the single turnover of an enzyme.

The complete solution to the kinetic equation for nucleotide fluorescence quenching on addition of pyruvate to the late dehydrogenase-NADH complex modifies previous interpretations of such experiments.     

Determination of the MurD mechanism through crystallographic analysis of enzyme complexes.

UDP -N- acetylmuramoyl- L -alanine: D -glutamate (MurD) ligase catalyses the addition of d -glutamate to the nucleotide precursor UDP -N- acetylmuramoyl- L -alanine (UMA). The crystal structures of three complexes of Escherichia coli MurD with a variety of substrates and products have been determined to high resolution. These include (1) the quaternary complex of MurD, the substrate UMA, the product ADP, and Mg2+, (2) the quaternary complex of MurD, the substrate UMA, the product ADP, and Mn2+, and (3) the binary complex of MurD with the product UDP - N- acetylmuramoyl- L -alanine- D -glutamate (UMAG). The reaction mechanism supported by these structures proceeds by the phosphorylation of the C-terminal carboxylate group of UMA by the gamma-phosphate group of ATP to form an acyl-phosphate intermediate, followed by the nucleophilic attack by the amino group of D-glutamate to produce UMAG. A key feature in the reaction intermediate is the presence of two magnesium ions bridging negatively charged groups.     

Mixtures of tight-binding enzyme inhibitors. Kinetic analysis by a recursive rate equation.

When two or more tight-binding inhibitors are present in an enzyme assay, the equation that relates the initial velocity v to the concentration of reactants cannot be written in an algebraically explicit form. Rather, for n inhibitors it is an implicit polynomial equation of degree n + 1 with respect to v. The complexity of the polynomial coefficients dramatically increases with each added inhibitor. Solving the transcendental rate equation by traditional methods of numerical mathematics has proven tedious because of the sensitivity of these methods to initial estimates and because of the existence of multiple roots. However, the equation can be rearranged into a convenient recursive form, one in which the velocity appears on both sides and the solution is found iteratively. The algebraic form of the recursive rate equation is remarkably simple and differs from the rate equation for classical rather than tight-binding inhibition only by an added term. The numerical stability and the speed of convergence were tested on the case of two competitive inhibitors. Initial estimates of velocity that spanned 12 orders of magnitude converged within five iterations. The velocities computed with the recursive method for a single tight-binding inhibitor were identical with the values predicted by the Morrison equation. The method is used to analyze experimental data for the inhibition of rat liver dihydrofolate reductase by mixtures of the anticancer drug methotrexate and its metabolic precursor form, methotrexate-alpha-aspartate (a prodrug).     

Structural and functional analysis of the rat malic enzyme gene promoter.

We have characterized sequences of genomic DNA 5' to the coding region of the rat malic enzyme gene. This sequence possesses neither TATA nor CCAAT sequences in their usual positions but is rich in GC residues. Sequences similar to those found in the regulatory regions of other genes are discussed. Deletion analyses have revealed that sequences +1 to -41 are sufficient to initiate expression, although inclusion of information up to -177 is necessary for maximal promoter activity.     

Physical map of bacteriophage BF23 DNA: restriction enzyme analysis.

Cleavage maps of bacteriophage BF23 DNA have been constructed for the restriction endonucleases SalI (3 fragments), BamHI (5 fragments), EcoRI, (8 fragments), BalI (13 fragments), and HpaI (49 fragments, 32 of which have been ordered). The maps were determined by (i) analysis of deletion mutants, (ii) digestion with two endonucleases, (iii) digestion of isolated fragments with a second enzyme, (iv) analysis of partial digests, and (v) digestion after treatment with lambda exonuclease.